The oral microbiome profile of Pakistani infants characterized by 16S rRNA amplicon sequencing

The oral microbiome is the second most complex and diverse ecosystem in the human body. A number of longitudinal studies assessing oral microbiome development in diverse populations has been reported recently. However, oral microbiome development in vulnerable populations such as infants who are at risk of malnutrition is rarely explored. The current study aims to assess oral bacterial community development and associated factors in Pakistani infants residing in malnutrition endemic areas of Pakistan. Data and oral swab samples were collected from infants (<i>n</i> = 71) at baseline (age <28 days) and 3-months follow-up (<i>n</i> = 65) followed by DNA extraction, PCR amplification and 16S rRNA amplicon sequencing on a DNBSEQ-G400 platform. Of the total 136 samples, 119 samples were successfully sequenced and analyzed further. Bioinformatics and statistical analyses were performed using Cutadapt, FLASH and R. Overall, the <i>Bacillota</i> (formerly known as <i>Firmicutes</i>) was the predominant bacterial phylum, accounting for 87.6 % relative abundance at baseline and 84.3 % at 3-months. The <i>Streptococci</i> and <i>Veillonella</i> were the predominant bacterial genera with 66.9 % and 13.4 % relative abundance at baseline and 55.4 % and 26.1 % at 3-months, respectively. This study provides the first comprehensive insights into oral bacterial community development of vulnerable infants at risk of malnutrition. The data can be used to longitudinally assess oral microbiome develop during early infancy and associated maternal, infant and environmental factors. Sequencing data are deposited in the NCBI Sequence Read Archive as BioProject PRJNA1303979.